RRNA comparative sequence analysis

FIGURE 12.39 The proposed secondary structure for E. coli 16S rRNA, based on comparative sequence analysis in which the folding pattern is assumed to be conserved across different species. The molecule can be subdivided into four domains—I, II, III, and IV—on the basis of contiguous stretches of the chain that are closed by long-range base-pairing interactions. I, the 5 -domain, includes nucleotides 27 through 556. II, the central domain, runs from nucleotide 564 to 912. Two domains comprise the 3 -end of the molecule. Ill, the major one, comprises nucleotides 923 to 1391. IV, the 3 -terminal domain, covers residues 1392 to 1541. 

Holoman TRP, MA Elberson, LA Cutter, HD May, KR Sowers (1998) Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-orf/io-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol 64 3359-3367. 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Oerther DB, Danalewich J, Dulekgurgen E (1998) Bioaugmentation of sequencing batch reactors for biological phosphoms removal comparative rRNA sequence analysis and hybridization with oligonucleotide probes. Wat Sci Technol 37 469 173... 

The structures of the rRNAs were generated and sequences compared using the University of Wisconsin Genetics Computer Group Nucleic Acid sequence analysis package29 and the University of Georgia Biological Structure and Sequence Computation Facility. 

Purkhold, U., Pommerening-Roser, A., Juretschko, S., Schmid, M. C., Koops, H. P., and Wagner, M. (2000). Phylogeny of aU recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis Implications for molecular diversity surveys. Appl. Environ. Microbiol. 66, 5368—5382. 

Gremion, F., Chatzinotas, A., and Harms, H. (2003). Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ. Microbiol. 5, 896-907. 

Chean R, Kotsanas D, Francis MJ, Palombo FA, Jadhav SR, Awad MM, Lyras D, Korman TM, Jenkin GA. Comparing the identification of Clostridium spp. by two Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry platforms to 16S rRNA PCR sequencing as a reference standard A detailed analysis of age of culture and sample preparation. Anaerobe. 2014 30 85 9. doi 10.1016/j.anaerobe.2014.09.007. 

A list of primer sequences that may be of universal applicability for the large subunit rRNA molecule is given in Table I. Primers having a more restricted range of utilization may also be selected, particularly when analyzing portions of the rRNA molecule that have already been subjected to an intensive comparative analysis. It is noteworthy that the very large collection of partial sequences7 21-22 (more than 100) for the 5 terminal... 

Fig. 4. Primer extension analysis of rRNAs isolated from four plant species treated with dimethyl sulfate. Sequencing lanes are indicated as A, T, G, and C. A plus sign (+) over the lane denotes RNA prepared from DMS-treated tissues a minus (—) denotes RNA isolated from mock-treated tissues. The nucleotide numbers are the coordinates at which primer extension reactions terminate (see Figs- 3 and 5A). The position of the modified base in the sequence of the 18 S rRNA is determined by comparing novel bands in the DMS-reacted RNA with the sequencing ladder and adding one nucleotide (see Fig. 2 for details). Various regions of the RNA are shown for the different plant species. Several sites of chain termination arising from nascent structure are also evident.

Both genotypic (primary structural) and functional properties of the archaeal translational machinery confirm the distinctness of the archaea originally inferred from comparative analysis of rRNA sequences. 

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